I'm not sure if this is hard to answer without the original data, but let's give it a go.
I'm calculating the difference in proportions for two diagnostic methods:
outcome test 0 1 method1 22 30 method2 18 39
Using R and
prop.test(c(30, 39), c(52, 57)) gives me a p = 0.3361.
Using R and the infer package "Two categorical (2 level) variables" gives me p = 0.250.
Is such a big difference to be expected when using permutation, or am I doing something wrong?